Querying PubMed using R

I've seen talks over the years where the speaker shows a bar chart with the number of articles in PubMed that contain a certain keyword and tallied per year. In most of the cases the speaker was trying to illustrate the growing number of articles that contain the keyword. Here I try to do the...

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Probability

The fundamental idea of inferential statistics is determining the probability of obtaining the observed data when we assume the null hypothesis is true. For example, if we roll a die 10 times and got 10 sixes, what is the probability of observing this result if we assume the null hypothesis that the die was fair?...

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Using Gviz

Updated: 2013 November 15th A while ago I asked on Twitter, what are some tools that people use to visualise hundreds of bam files. One of the suggestions was Gviz (thanks Sebastian!) and I had a quick glimpse at the Bioconductor package and the plots looked really great! Here I use Gviz to plot features...

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Transcription factor binding site prediction

Updated 2013 December 17th to include JASPAR I have a simple task: given a short DNA sequence and I want to know if there are any potential transcription factor binding sites within this sequence. I looked online and found this transcription factor binding site prediction tool called TFSEARCH. It's very straight-forward; all you have to...

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Position weight matrix

The process of transcription, is influenced by the interaction of proteins called transcription factors (TFs) that bind to specific sites called Transcription Factor Binding Sites (TFBSs), which are proximal or distal to a transcription starting site. TFs generally have distinct binding preferences towards specific TFBSs, however TFs can tolerate variations in the target TFBS. Thus...

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